Contacts of the helix formed by residues 79 - 96 (chain A) in PDB entry 3SRH


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 79 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLY*     1.3    74.1    -      -       -      -
     80A  HIS*     1.3    68.0    +      -       -      +
     81A  GLU*     3.7     8.1    +      -       -      +
     82A  TYR*     3.4    20.9    +      -       -      +
     83A  HIS*     3.1    27.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE*     4.5    11.2    -      +       -      -
     78A  GLY      5.2     2.0    -      -       -      -
     79A  THR*     1.3    76.2    -      -       -      +
     81A  GLU*     1.3    60.0    +      -       -      +
     83A  HIS*     3.5     1.5    +      -       -      -
     84A  ALA*     2.9    32.3    +      -       -      +
    223A  LYS*     5.2     2.7    +      -       -      -
    226A  GLN*     4.0    17.9    +      -       +      +
    227A  ASP*     2.8    28.4    +      -       -      -
    230A  PHE*     3.3    52.5    -      +       +      +
----------------------------------------------------------
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Residues in contact with GLU 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  THR*     3.7     7.1    +      -       -      +
     80A  HIS*     1.3    78.3    -      -       -      +
     82A  TYR*     1.3    62.7    +      -       -      +
     84A  ALA*     3.3     6.0    +      -       -      +
     85A  GLU*     3.1    28.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE      5.8     1.1    -      -       -      -
     51A  GLY*     5.4     5.4    -      -       -      -
     52A  PRO*     3.8    29.6    -      -       +      +
     55A  ARG*     3.4    54.8    +      -       -      +
     78A  GLY*     4.7    13.7    -      -       -      -
     79A  THR*     3.4    24.2    +      -       -      +
     80A  HIS      3.3     0.2    -      -       -      -
     81A  GLU*     1.3    79.8    -      -       -      +
     83A  HIS*     1.3    71.2    +      +       -      +
     85A  GLU*     3.5     4.8    +      -       -      +
     86A  THR*     2.9    29.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE      5.7     4.0    -      -       -      -
     73A  LEU*     3.3    28.9    -      -       +      +
     74A  ASN      3.5    20.8    +      -       -      -
     75A  PHE*     3.8    38.5    -      +       +      -
     77A  HIS      2.9    22.2    +      -       -      -
     78A  GLY*     3.7    12.4    -      -       -      -
     79A  THR      3.1    23.2    +      -       -      +
     80A  HIS*     4.0     3.1    -      +       -      +
     82A  TYR*     1.3    87.3    -      +       -      +
     84A  ALA*     1.3    60.0    +      -       -      +
     86A  THR*     3.2     8.1    +      -       -      +
     87A  ILE*     3.0    33.6    +      -       -      +
    230A  PHE*     4.3     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  HIS      2.9    19.8    +      -       -      +
     81A  GLU*     3.7     6.5    -      -       -      +
     83A  HIS*     1.3    75.8    -      -       -      +
     85A  GLU*     1.3    58.4    +      -       -      +
     87A  ILE*     3.4     3.3    +      -       -      +
     88A  LYS*     2.9    27.8    +      -       -      +
    230A  PHE*     4.0    10.3    -      -       +      -
    234A  GLN*     3.8    26.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ARG*     2.9    26.7    +      -       -      +
     81A  GLU*     3.1    20.5    +      -       +      +
     82A  TYR*     3.7     5.0    -      -       -      +
     83A  HIS      3.3     0.2    -      -       -      -
     84A  ALA*     1.3    72.9    -      -       -      +
     86A  THR*     1.3    55.9    -      -       -      +
     88A  LYS*     3.3    17.7    +      -       -      +
     89A  ASN*     2.7    57.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     3.7    39.7    -      -       +      +
     55A  ARG*     3.0    28.5    +      -       +      +
     60A  LEU*     4.6     0.4    -      -       +      +
     73A  LEU*     4.3    16.8    -      -       +      -
     82A  TYR*     2.9    19.5    +      -       -      -
     83A  HIS*     3.4    13.7    +      -       -      +
     85A  GLU*     1.3    78.5    -      -       -      +
     87A  ILE*     1.3    52.3    +      -       -      +
     89A  ASN*     3.3     7.1    +      -       -      +
     90A  VAL*     2.8    34.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  LEU*     3.7    22.2    -      -       +      -
     75A  PHE*     5.6     1.3    -      -       +      -
     83A  HIS      3.0    20.0    +      -       -      +
     84A  ALA      3.7     4.5    -      -       -      +
     85A  GLU      3.2     0.2    -      -       -      -
     86A  THR*     1.3    73.2    -      -       -      +
     88A  LYS*     1.3    61.8    +      -       -      +
     90A  VAL*     3.4     7.2    +      -       -      +
     91A  ARG*     3.0    67.6    +      -       -      +
    109A  VAL*     4.2    23.6    -      -       +      -
    111A  LEU*     6.5     0.2    -      -       +      -
    230A  PHE*     4.4    12.6    -      -       +      -
    234A  GLN*     4.0    31.4    -      -       +      +
    236A  VAL*     4.7     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ALA      2.9    18.1    +      -       -      +
     85A  GLU*     3.4    17.7    -      -       -      +
     87A  ILE*     1.3    77.5    -      -       -      +
     89A  ASN*     1.3    64.7    +      -       -      +
     91A  ARG*     3.3     7.2    +      -       +      +
     92A  THR*     2.9    42.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ARG*     3.3    35.8    +      -       -      +
     56A  SER*     4.3     4.2    -      -       -      +
     57A  VAL*     3.5    29.4    -      -       +      +
     60A  LEU*     3.7     4.1    -      -       +      +
     85A  GLU*     2.7    44.1    +      -       -      +
     86A  THR      3.6     4.9    -      -       -      +
     88A  LYS*     1.3    80.9    +      -       -      +
     90A  VAL*     1.3    64.1    +      -       -      +
     92A  THR*     4.4     1.3    +      -       -      -
     93A  ALA*     3.1    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     4.6     6.1    -      -       +      -
     60A  LEU*     3.8    26.7    -      -       +      -
     64A  ILE*     4.9     0.6    -      -       +      +
     68A  MET*     5.4     2.0    -      -       +      -
     71A  ALA*     4.0    20.6    -      -       +      -
     73A  LEU*     5.6     2.0    -      -       +      -
     86A  THR*     2.8    27.1    +      -       +      +
     87A  ILE*     3.7     7.6    -      -       -      +
     88A  LYS      3.4     0.2    -      -       -      -
     89A  ASN*     1.3    72.0    -      -       -      +
     91A  ARG*     1.3    55.6    +      -       +      +
     93A  ALA*     3.3     4.2    +      -       -      +
     94A  THR*     2.7    50.0    +      -       -      +
    107A  VAL*     4.3    16.6    -      -       +      +
    109A  VAL*     4.3    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  ILE*     3.0    43.3    +      -       -      +
     88A  LYS*     3.7     6.5    -      -       -      +
     90A  VAL*     1.3    77.4    -      -       +      +
     92A  THR*     1.3    56.9    +      -       -      +
     94A  THR*     4.3     5.8    -      -       -      -
     95A  GLU*     2.7    49.0    +      -       +      +
    109A  VAL*     4.4    18.3    -      -       +      +
    234A  GLN*     2.8    33.1    +      -       -      +
    235A  ASP*     3.1    26.7    +      -       -      +
    236A  VAL*     4.7     0.2    -      -       -      +
    237A  ASP*     5.6     0.4    +      -       -      -
    460A  ARG*     5.8     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  VAL*     3.7    24.8    -      -       +      +
     61A  LYS*     5.5     2.0    -      -       -      +
     88A  LYS*     2.9    36.1    +      -       -      +
     89A  ASN*     3.9     5.5    +      -       -      -
     91A  ARG*     1.3    71.7    -      -       -      +
     93A  ALA*     1.3    62.4    +      -       -      +
     95A  GLU*     3.5     3.3    +      -       -      +
     96A  SER*     3.1    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  VAL*     3.8    15.0    -      -       +      +
     60A  LEU*     3.7    27.8    -      -       +      -
     61A  LYS*     3.8    14.5    -      -       +      +
     64A  ILE*     3.9     4.5    -      -       +      -
     89A  ASN      3.1    20.0    +      -       -      +
     90A  VAL      3.6     2.9    -      -       -      +
     92A  THR*     1.3    76.4    -      -       -      +
     94A  THR*     1.3    61.5    +      -       -      +
     96A  SER*     2.7    25.7    +      -       -      -
     97A  PHE*     3.4    10.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE*     3.7    11.2    -      -       -      +
     90A  VAL*     2.7    33.3    +      -       -      +
     91A  ARG*     3.7     7.4    -      -       -      -
     93A  ALA*     1.3    75.0    -      -       -      +
     95A  GLU*     1.3    63.1    +      -       -      +
     96A  SER      3.1     4.2    +      -       -      -
     97A  PHE*     3.4    15.6    +      -       -      +
    104A  TYR*     3.5    30.3    -      -       -      +
    105A  ARG      3.9     9.6    -      -       -      +
    107A  VAL*     3.5    44.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ARG*     2.7    33.5    +      -       +      +
     92A  THR*     3.9     2.9    -      -       -      +
     94A  THR*     1.3    76.0    -      -       -      +
     96A  SER*     1.3    56.0    +      -       -      +
     97A  PHE      3.1     5.2    -      -       -      -
     98A  ALA*     3.2    36.8    +      -       +      +
     99A  SER      4.6     0.7    +      -       -      -
    104A  TYR*     2.6    29.5    +      -       -      -
    474A  LYS*     5.1     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  LYS*     3.6    29.3    -      -       -      +
     92A  THR*     3.1    16.6    +      -       -      -
     93A  ALA      2.7    17.2    +      -       -      -
     94A  THR      3.1     0.2    -      -       -      -
     95A  GLU*     1.3    76.8    -      -       -      +
     97A  PHE*     1.3    71.2    +      -       -      +
     98A  ALA      3.4     0.4    -      -       -      -
     99A  SER*     4.4     9.4    +      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il